If you say so. For me, field map correction is all about getting good
registrations (i.e. geometric undistortions), I assume that the signal
effects must be minimized in other ways (e.g. parallel imaging).
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Michael Harms
Sent: Thursday, October 14, 2010 5:19 PM
To: [log in to unmask]
Subject: Re: [FSL] effectiveness of field correction as a function of phase
encoding direction
Ok, so applying field map correction with A>>P phase encoded data is
still beneficial. BUT, is it considerably more beneficial if the
original BOLD data had been acquired P>>A instead?
thanks,
-MH
On Thu, 2010-10-14 at 17:09 -0500, Matt Glasser wrote:
> It isn't just signal compression. If you compare a distorted to
undistorted
> dataset you will see that there are geometric effects outside of the
region
> with dephasing, compression, and rarefaction. The correct way to deal
with
> this is to undistort the data and then use only 6 parameters to register
the
> BOLD to the T1. The way your processing stream probably works is that it
> uses 12 parameters and probably partially compensates for the distortion,
> however your registration in other brain areas will also be off because
you
> are doing a linear correction of a nonlinear phenomenon.
>
> It matters most if you care about having exact alignment between your BOLD
> data and T1, for example if you are going to do surface analysis.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Michael Harms
> Sent: Thursday, October 14, 2010 4:53 PM
> To: [log in to unmask]
> Subject: Re: [FSL] effectiveness of field correction as a function of
phase
> encoding direction
>
> Thanks for the tutorial. So, as a practical matter, does one get
> anywhere near the same benefit in correcting BOLD problems in the
> frontal cortex when applying field map correction to data collected with
> A>>P phase encoding, vs. P>>A phase encoding?
>
> We have a bunch of BOLD data collected with A>>P phase encoding on a
> Siemens Trio, for which we also collected a field map in that session.
> However, we have yet to work the field map correction into our actual
> processing protocol. Now I'm wondering if we'll really get much benefit
> of applying a field map correction to that data given the rather
> pronounced signal compression that you can get in frontal cortex when
> using A>>P phase encoding.
>
> thanks,
> -MH
>
> On Thu, 2010-10-14 at 17:24 +0100, Jesper Andersson wrote:
> > Dear Michael,
> >
> > > Thanks Matt. But I'm still a little bit puzzled about the "limits" of
> > > field mapping correction. You wrote that it is good at "geometrical
> > > distortion correction, but less good at correction of intensities from
> > > signal stretching or compression". Aren't those just variations
> > > along a
> > > continuum of the same underlying phenomenon?
> >
> > partially they are, and partially they are not. For DTI (spin-echo
> > EPI) the intensity distortions have a simple relationship to the
> > geometric distortions (e.g. if you take two voxels worth of signal and
> > squeeze into on voxel you will observe double the intensity).
> >
> > For those scans it would in principle be possible to exactly restore
> > the true images. BUT, because the images are discrete we end up in
> > situations where the intensity from several "object voxels" is
> > squeezed into one image voxel, and in those cases we do not have the
> > information that we need. It would be equivalent to try to deduce a
> > sample from the sample mean. A way around that, as has been suggested
> > in this thread, is to collect data with different traversals of k-
> > space (e.g. phase-encoding ant-post and post-ant) which means that for
> > each area that has been squashed in one acquisition the corresponding
> > area will have been stretched in the other acquisition. The
> > information from the two scans can then be combined to yield a
> > reasonable estimate of the true intensity values. We currently have a
> > internal release of software for doing that, and will release it as a
> > part of FSL when we are happy with how it works.
> >
> > For fmri (gradient echo EPI) the situation is much more tricky. The
> > stretching/compression of intensities is still present, but we now
> > also have signal loss due to de-phasing within the voxel. This de-
> > phasing is a highly non-linear function of the partial derivatives of
> > the field in the phase-encode and slice-select directions and there is
> > currently no method available for estimating it.
> >
> > Hope this helped clarifying things a little.
> >
> > Jesper
> >
> >
> >
> >
> > >
> > > thanks,
> > > -MH
> > >
> > > On Wed, 2010-10-13 at 11:44 -0500, Matt Glasser wrote:
> > >> Hi Michael,
> > >>
> > >> It is certainly true that once signal from multiple voxels has been
> > >> compressed into a single voxel, it is hard to put it back with a
> > >> field map
> > >> alone. For diffusion data, phase up / phase down corrections have
> > >> a better
> > >> chance of dealing with this issue, as you have the data both
> > >> compressed and
> > >> rarified and can figure out what the undistorted image would have
> > >> looked
> > >> like. It is not possible to do this with BOLD data, as you can't
> > >> acquire a
> > >> run and then a second run with the phase encode direction flipped
> > >> and unwarp
> > >> and average them (which is what happens with the diffusion data).
> > >> That
> > >> being said, perhaps if you acquired the slices of phase up and
> > >> phase down
> > >> interleaved with one of these faster TR sequences you could pull
> > >> off phase
> > >> up / phase down correction on BOLD data (though you would want to
> > >> run slice
> > >> timing correction first).
> > >>
> > >> If I recall correctly from a conversation Jesper and I had, R/L (or
> > >> L/R)
> > >> phase encode direction actually have the least severe distortions,
> > >> but
> > >> people don't like them because the distortions are not
> > >> symmetrical. If you
> > >> were most interested in stuff in the orbitofrontal region, it might
> > >> make
> > >> sense to use a phase encode that stretches rather than compresses
> > >> this
> > >> region (though of course other regions would be compressed instead).
> > >>
> > >> The field map is good at geometrical distortion correction, but
> > >> less good at
> > >> correction of intensities from signal stretching or compression (or
> > >> outright
> > >> loss).
> > >>
> > >> Peace,
> > >>
> > >> Matt.
> > >>
> > >> -----Original Message-----
> > >> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> > >> Behalf
> > >> Of Michael Harms
> > >> Sent: Wednesday, October 13, 2010 11:25 AM
> > >> To: [log in to unmask]
> > >> Subject: [FSL] effectiveness of field correction as a function of
> > >> phase
> > >> encoding direction
> > >>
> > >> Hello,
> > >> Is the effectiveness of field correction for compensating for B0
> > >> distortions at least partially dependent on the phase encoding
> > >> direction
> > >> used to acquire the BOLD or DTI data that is to be corrected?
> > >>
> > >> To use Siemen's parameter lingo, a "P>>A" phase encoding direction
> > >> stretches signal from frontal cortex outward (anteriorly, into empty
> > >> space), whereas "A>>P" (which is unfortunately Siemen's default)
> > >> compresses signal from frontal cortex (i.e., moves frontal signal
> > >> posteriorly, onto existing brain). It seems that once signal from
> > >> multiple voxels is compressed into 1 voxel that not much correction
> > >> would be possible... Is that indeed the case?
> > >>
> > >> thanks,
> > >> -MH
> > >>
> > >>
> > >
|